The port of Paxoi is located in the Gaios area in the southern part of the island and is connected by ferry to Igoumenitsa, Corfu and Antipaxoi.

The port is protected by two islands, the island of Panagia and the island of Agios Nikolaos, creating a floating corridor between them.

There is also a marina where small fishing and tourist boats find shelter, which during the tourist season regularly go to Antipaxos, but also on routes around the island.